omicverse-single-cell-batch-integration

What problem does it solve?

Automates batch integration for preprocessed single-cell AnnData across multiple backends, enabling side-by-side comparison and benchmarking.

Core Features & Use Cases

• Supports integration backends Harmony, Combat, Scanorama, scVI, CellANOVA, and Concord from a single callable workflow, streamlining technology comparisons.
• Enables benchmarking by producing both integrated embeddings and non-integrated references for evaluation across methods.
• Real-world use: compare batch correction strategies on a preprocessed AnnData with a batch column to select the best backend for downstream analysis.

Quick Start

Run the preprocessed AnnData through the batch-integration skill to compare Harmony, Combat, and ScVI backends and optionally run the Benchmarker.